| File menu item | Description |
| Load simulation data file (STODE output) | Choosing this menuentry brings up a file manager, so that the user can choose a file containing numerical simulation data. |
| Load simulation data file (COPASI output) | Choosing this menuentry brings up a file manager, so that the user can choose two files where the first one should contain some metadata about the simulation and the second one should contain the rest of the data, i.e. the numbers describing the concentration or the number of molecules for each compount at every given (simulated) point in time. (see Copasi file format description) |
| Load reaction graph | Clicking here brings up a file manager, with which the user can select a network graph file to load. In the current version the graph should be in either "pure" SBML, or, when created with the ReactionLayouter tool, in the extended SBML format created by that tool or the binary format generated by the Java serialization protocol. Please note that using the latter format can be hazardous (see below). |
| Create movie (SVG) | Exports the whole animation as a SVG movie (NOT FULLY IMPLEMENTED YET) |
| Exit | Exit SimWiz. |
| Settings menu item | Description |
| Print warnings | Will enable that whenever a simulation step during an animation is shown much later (> 50 ms) then the time it was scheduled for, a warning is printed out to standard out. |
| Leave late steps out | Sets the system not to display any simulation steps that within an animation would be displayed much too late (> 50ms beyond schedule). |
| Insert extra graph when recording images | When image recording is enabled (see below) all images of an animation, each showing a single simulation state, are written to a file. If this option is enabled, each image is expanded by a picture of the network graph in its "original" state, i.e. with all nodes having minimum size. This can help in keeping hold of the network topology during an animation. |
Camera button: When pressing this button a snapshot is taken from the current animation state, i.e. the image currently shown in the graph panel is added to a list of images which are displayed side by side in the so-called SnapshotViewer. This viewer is automatically opened when the button is pressed (except for the state, when the viewer is in it's iconified state).
Video Camera button: If the user clicks on this button, the recording facility of SimWiz is turned on. This means every image (with each representing a simulation state) created during an animation process or while the user single-steps through the simulation data, is written to file in png format. Via a file manager, the user is asked to specify a directory for the images to be written to. These images can be taken later to create a film (e.g. an animated gif).
Clicking on the video camera button again, will switch recording off.
| Menu item | Description |
| Zoom in | The whole network graph is scaled up by a factor of 1.5 |
| Zoom out | The whole network graph is scaled down by a factor of 2/3. |
| Zoom free (> 0) | The whole network graph is scaled by a factor that can be freely chosen by the user. |
| Fit into panel | The network graph is scaled in a way that the whole picture fits into the given panel. That usually means that the graph is scaled in x- and y-direction by different scale factors. This option should be used carefully, because the non-uniform scaling is irreversible. |
| Show "simulated" compound names only / Show all compound names | Toggles between two states: Selecting the first option, only the names of those compounds (i.e. nodes in the network) listed in the simulation data file are shown. Selecting the second option, all names are shown in the graph panel. |
| Modify min/max node size(s) | In "size mode" the size of a each circle represents the concentration or the number of molecules of a certain compound. The values specified in the simulation data file are scaled between a minimum and a maximum value (for the diameter or the area of a circle). The values for the minimum and the maximum diameter can be changed interactively when choosing this menuentry. This menuentry only applies in "size mode". In "color mode" there will be no effect when changing the min/max values. |
| Change font size for nodes | Allows the modification of the font size of the compound names. |
| Change size of pseudonodes | In SimWiz, the graphical representation of each reaction is given by a line connectiong two so-called pseudonodes. There are lines connecting the substrates with the first pseudonode and lines connecting the products with the second pseudonode. During animation the sizes of the pseudonodes stay constant. Here, the user can change the pseudonode size. If he or she does not want to see the pseudonodes at all, the size should be set to 0. |
| Button/Control Item | Description |
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Rewind: takes the animation back to the start of the simulation data file |
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Previous: steps one step backward |
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Start: starts the animation process |
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Stop: pauses the animation process |
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Next: steps one step forward |
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Moving the slider knob with the mouse (left mouse button) along the slider takes the animation to the time point where the mouse was released. |
| Parameter item | Description |
| Frame rate (k frames / sec) | In equidistant scheduling mode (see below), each simulation state (which is defined by the values for the concentration/number of molecules at a certain point of time) is used to create one animation frame. In the animation a constant frame rate is used, i.e. the states are shown at equidistant time steps. The user can choose between 1, 2, 5, 10, and 20 frames/second. This, of course, only is kept when the user's machine is fast enough. |
 | This slider can only be seen when the scheduling mode is set to "scaled". Moving the slider's knob with the mouse the user can select a speed factor for the animation. The 1:1 value in the middle of the slider means that SimWiz tries to show the simulation states represented by the animation frames at the speed that is defined by the time points specified in the simulation data file. Choosing a point left to the 1:1 value slows down the animation, choosing a point to the right speeds up the process. The speed factor can be chosen from a logarithmic scale with a minimum value of 0.001 (* real-time speed) and a maximum value of 1000 (* real-time speed). |
| Scheduling Mode | The animation consists of a sequence of single frames, with each representing a single simulation state. In equidistant scheduling mode, the frames are shown with a constant frame rate, i.e. the current frame is replaced by the next one after a constant time interval. This is also the case when the simulation data results from a stochastic simulation where the temporal distance between any two consecutive simulation steps can differ substantially. In scaled scheduling mode, SimWiz tries to mimic real time behaviour by analyzing the time points that are specified for each simulation step in the data file. The temporal differences between any two steps is used to show the corresponding frames in the according temporal distance. Depending on the speed factor the user has chosen, these values are scaled appropriately. |
| Mapping Mode | SimWiz uses two different visualization schema to illustrate the concentration/number of molecules of each compound. In size mode, the corresponding values are mapped to the diameter or the area (choice in the submenu) of the circles representing the compounds. All values are scaled to fit into the interval between a minimum and a maximum value (which can be changed in the graph panel). In color mode the size of the circles remains the same and the values of the concentration/number of molecules are mapped to a color scale. Blue thereby means a minimum value and red a maximum value. Choosing the color mode will bring up a legend within the graph panel that can be moved by dragging the mouse when the mouse pointer is on the legend. |
| Node Scaling Mode | For each compound covered by the simulation data file there is a maximum value for the concentration/number of molecules. This maximum value is found by looking at all values in the file. In the default individual mode each compound is taken individually and all values are scaled to fit the minimum and maximum value of the size (diameter or area) of the circle representing the compound or are transformed to the corresponding value within the interval of the minimum and maximum color value (see mapping mode above). If the user chooses the global mode, everything is scaled to fit into the interval of the overall minimum and maximum value over all compounds. |
There also is a background menu (right mouse click) with some settings for the whole list of compounds:
| Menu item | Description |
| Select all compounds | Select all valid compounds (i.e. those which appear in the graph) for animation in the graph panel. |
| Choose color for all compounds | The user can choose a color which is used for all compounds which are selected (in the checkbox) for animation. |
| Toggle number format style | The user can switch between two styles in which the numbers representing the values for the concentration / number of molecules are written. The default style is the decimal style (e.g. 1234.567) and the other one is the scientific notation (e.g. 1.23E3) with two positions (at maximum) after the decimal point. |
Warning: It can be problematic to use the binary format (i.e. the format produced by the Java serialization protocol when calling the method writeObject(java.io.ObjectOutputStream out)) as long there is ongoing work on SimWiz. Whenever one of the source files which has to do with the graph data structure is changed (i.e. gets a new field variable or a new method is introduced), all files produced by serializing the data get a new so called serialVersionUID. That means that old files can't be read with a newer version of SimWiz.
If you want to use the ReactionLayouter tool for creating sophisticated network layouts, it is recommendable to additionally save the layout always in (extended) SVG. This should work (i.e. can always be read back to the tool) regardless whether the layout of a given graph imported from SBML was changed or whether a new graph was created from scratch.
